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Crystal Structure of C151S+H178N mutant of Glyceraldehyde-3-phosphate dehydrogenase 1 (GAPDH1) from Staphylococcus aureus MRSA252 complexed with NAD at 2.2 angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3H48
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 0.1M Tris-HCl pH8.5, 30% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.83 32.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.654 α = 90 b = 94.315 β = 106.02 c = 87.981 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ Varimax mirrors 2009-11-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.2 84.56 90.1 0.061 9.6 2.41 47907 45.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.28 93.2 0.264 2.9 2.21 4906
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3H48 2.2 25.84 47902 2438 90.05 0.208 0.205 0.2102 0.258 0.2605 RANDOM 38.235
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 1.3 -1.14 -0.68 -1.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.922 r_dihedral_angle_4_deg 23.715 r_dihedral_angle_3_deg 16.136 r_dihedral_angle_1_deg 7.067 r_scangle_it 4.692 r_scbond_it 2.749 r_angle_refined_deg 1.676 r_mcangle_it 1.436 r_mcbond_it 0.737 r_chiral_restr 0.108
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.922 r_dihedral_angle_4_deg 23.715 r_dihedral_angle_3_deg 16.136 r_dihedral_angle_1_deg 7.067 r_scangle_it 4.692 r_scbond_it 2.749 r_angle_refined_deg 1.676 r_mcangle_it 1.436 r_mcbond_it 0.737 r_chiral_restr 0.108 r_bond_refined_d 0.017 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10079 Nucleic Acid Atoms Solvent Atoms 316 Heterogen Atoms 175
Software Software Software Name Purpose d*TREK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection d*TREK data reduction